EHV-1 Canonic Transcript dynamics (TSS ~ TES)
Balázs Kakuk
## Error in library(future.apply) :
## there is no package called 'future.apply'Project info
Samples: dcDNA Seq
pychopper: no
mapping version: v6
LoRTIA: yes (stranded only output)
Canonic Transcript dynamics (TSS ~ TES)
Those reads were counted only, where both the 3-prime AND the 5-prime adapters were “correct” (according to LoRTIA)
When counting with either adapters, the clustering grouped ORF64 together with two late genes
Statistics of counts
Difference from mean
Varcoeff
Clustering of samples
## Bootstrap (r = 0.5)... Done.## Bootstrap (r = 0.59)... Done.## Bootstrap (r = 0.7)... Done.## Bootstrap (r = 0.79)... Done.## Bootstrap (r = 0.89)... Done.## Bootstrap (r = 1.0)... Done.## Bootstrap (r = 1.09)... Done.## Bootstrap (r = 1.2)... Done.## Bootstrap (r = 1.29)... Done.## Bootstrap (r = 1.39)... Done.
The sample 48h_3 stands out!
Filtering of samples
Clustering of genes into de-novo clusters using hierarchial clustering
Cluster memberships
## Bootstrap (r = 0.48)... Done.## Bootstrap (r = 0.59)... Done.## Bootstrap (r = 0.67)... Done.## Bootstrap (r = 0.78)... Done.## Bootstrap (r = 0.89)... Done.## Bootstrap (r = 1.0)... Done.## Bootstrap (r = 1.07)... Done.## Bootstrap (r = 1.19)... Done.## Bootstrap (r = 1.3)... Done.## Bootstrap (r = 1.37)... Done.Optimal number of clusters
Find the optimal number of clusters to cut the tree at and calculate
Clustering statistics: Cluster number: 5
## Key: <cluster>
## cluster gene si au bp se.si se.au
## <int> <char> <num> <num> <num> <num> <num>
## 1: 1 ORF1 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 2: 1 ORF2 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 3: 1 ORF3 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 4: 1 ORF4 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 5: 1 ORF8 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 6: 1 ORF9 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 7: 1 ORF11 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 8: 1 ORF14 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 9: 1 ORF18 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 10: 1 ORF19 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 11: 1 ORF20 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 12: 1 ORF21 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 13: 1 ORF22 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 14: 1 ORF23 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 15: 1 ORF24 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 16: 1 ORF25 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 17: 1 ORF26 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 18: 1 ORF28 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 19: 1 ORF29 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 20: 1 ORF31 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 21: 1 ORF33 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 22: 1 ORF34 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 23: 1 ORF35.5 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 24: 1 ORF36 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 25: 1 ORF37 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 26: 1 ORF38 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 27: 1 ORF39 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 28: 1 CTO 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 29: 1 ORF40 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 30: 1 ORF42 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 31: 1 ORF43 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 32: 1 ORF44 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 33: 1 ORF46 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 34: 1 ORF49 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 35: 1 ORF50 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 36: 1 ORF51 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 37: 1 ORF58 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 38: 1 ORF61 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 39: 1 ORF62 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 40: 1 ORF64_1 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 41: 1 ORF66_1 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 42: 1 ORF68 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 43: 1 ORF73 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 44: 1 ORF74 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 45: 1 ORF75 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 46: 1 ORF76 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 47: 2 ORF5 0.8361360 0.9524233 0.7136396 0.019845119 0.0077877677
## 48: 2 ORF7 0.8361360 0.9524233 0.7136396 0.019845119 0.0077877677
## 49: 2 ORF10 0.8361360 0.9524233 0.7136396 0.019845119 0.0077877677
## 50: 2 ORF17 0.8361360 0.9524233 0.7136396 0.019845119 0.0077877677
## 51: 2 ORF30 0.8361360 0.9524233 0.7136396 0.019845119 0.0077877677
## 52: 2 ORF53 0.8361360 0.9524233 0.7136396 0.019845119 0.0077877677
## 53: 2 ORF63 0.8361360 0.9524233 0.7136396 0.019845119 0.0077877677
## 54: 2 NOIR_2 0.8361360 0.9524233 0.7136396 0.019845119 0.0077877677
## 55: 3 ORF6 0.9921335 0.9984157 0.8993056 0.002040977 0.0005060408
## 56: 3 ORF65_1 0.9921335 0.9984157 0.8993056 0.002040977 0.0005060408
## 57: 3 ORF67_1 0.9921335 0.9984157 0.8993056 0.002040977 0.0005060408
## 58: 4 ORF12 0.4752019 0.7710846 0.6631909 0.036465996 0.0232411811
## 59: 4 ORF13 0.4752019 0.7710846 0.6631909 0.036465996 0.0232411811
## 60: 4 ORF15 0.4752019 0.7710846 0.6631909 0.036465996 0.0232411811
## 61: 4 ORF16 0.4752019 0.7710846 0.6631909 0.036465996 0.0232411811
## 62: 4 ORF27 0.4752019 0.7710846 0.6631909 0.036465996 0.0232411811
## 63: 4 ORF32 0.4752019 0.7710846 0.6631909 0.036465996 0.0232411811
## 64: 4 ORF35 0.4752019 0.7710846 0.6631909 0.036465996 0.0232411811
## 65: 4 ORF41 0.4752019 0.7710846 0.6631909 0.036465996 0.0232411811
## 66: 4 ORF48 0.4752019 0.7710846 0.6631909 0.036465996 0.0232411811
## 67: 4 ORF52 0.4752019 0.7710846 0.6631909 0.036465996 0.0232411811
## 68: 4 ORF54 0.4752019 0.7710846 0.6631909 0.036465996 0.0232411811
## 69: 4 ORF57 0.4752019 0.7710846 0.6631909 0.036465996 0.0232411811
## 70: 4 ORF59 0.4752019 0.7710846 0.6631909 0.036465996 0.0232411811
## 71: 4 ORF60 0.4752019 0.7710846 0.6631909 0.036465996 0.0232411811
## 72: 4 NOIR_1 0.4752019 0.7710846 0.6631909 0.036465996 0.0232411811
## 73: 4 ORF71 0.4752019 0.7710846 0.6631909 0.036465996 0.0232411811
## 74: 4 ORF72 0.4752019 0.7710846 0.6631909 0.036465996 0.0232411811
## 75: 5 ORF69 0.4866577 0.8510033 0.4742570 0.039463824 0.0177067445
## 76: 5 ORF70 0.4866577 0.8510033 0.4742570 0.039463824 0.0177067445
## cluster gene si au bp se.si se.au
## se.bp v c pchi
## <num> <num> <num> <num>
## 1: 0.002152081 -2.4868295 0.6511067 0.45180383
## 2: 0.002152081 -2.4868295 0.6511067 0.45180383
## 3: 0.002152081 -2.4868295 0.6511067 0.45180383
## 4: 0.002152081 -2.4868295 0.6511067 0.45180383
## 5: 0.002152081 -2.4868295 0.6511067 0.45180383
## 6: 0.002152081 -2.4868295 0.6511067 0.45180383
## 7: 0.002152081 -2.4868295 0.6511067 0.45180383
## 8: 0.002152081 -2.4868295 0.6511067 0.45180383
## 9: 0.002152081 -2.4868295 0.6511067 0.45180383
## 10: 0.002152081 -2.4868295 0.6511067 0.45180383
## 11: 0.002152081 -2.4868295 0.6511067 0.45180383
## 12: 0.002152081 -2.4868295 0.6511067 0.45180383
## 13: 0.002152081 -2.4868295 0.6511067 0.45180383
## 14: 0.002152081 -2.4868295 0.6511067 0.45180383
## 15: 0.002152081 -2.4868295 0.6511067 0.45180383
## 16: 0.002152081 -2.4868295 0.6511067 0.45180383
## 17: 0.002152081 -2.4868295 0.6511067 0.45180383
## 18: 0.002152081 -2.4868295 0.6511067 0.45180383
## 19: 0.002152081 -2.4868295 0.6511067 0.45180383
## 20: 0.002152081 -2.4868295 0.6511067 0.45180383
## 21: 0.002152081 -2.4868295 0.6511067 0.45180383
## 22: 0.002152081 -2.4868295 0.6511067 0.45180383
## 23: 0.002152081 -2.4868295 0.6511067 0.45180383
## 24: 0.002152081 -2.4868295 0.6511067 0.45180383
## 25: 0.002152081 -2.4868295 0.6511067 0.45180383
## 26: 0.002152081 -2.4868295 0.6511067 0.45180383
## 27: 0.002152081 -2.4868295 0.6511067 0.45180383
## 28: 0.002152081 -2.4868295 0.6511067 0.45180383
## 29: 0.002152081 -2.4868295 0.6511067 0.45180383
## 30: 0.002152081 -2.4868295 0.6511067 0.45180383
## 31: 0.002152081 -2.4868295 0.6511067 0.45180383
## 32: 0.002152081 -2.4868295 0.6511067 0.45180383
## 33: 0.002152081 -2.4868295 0.6511067 0.45180383
## 34: 0.002152081 -2.4868295 0.6511067 0.45180383
## 35: 0.002152081 -2.4868295 0.6511067 0.45180383
## 36: 0.002152081 -2.4868295 0.6511067 0.45180383
## 37: 0.002152081 -2.4868295 0.6511067 0.45180383
## 38: 0.002152081 -2.4868295 0.6511067 0.45180383
## 39: 0.002152081 -2.4868295 0.6511067 0.45180383
## 40: 0.002152081 -2.4868295 0.6511067 0.45180383
## 41: 0.002152081 -2.4868295 0.6511067 0.45180383
## 42: 0.002152081 -2.4868295 0.6511067 0.45180383
## 43: 0.002152081 -2.4868295 0.6511067 0.45180383
## 44: 0.002152081 -2.4868295 0.6511067 0.45180383
## 45: 0.002152081 -2.4868295 0.6511067 0.45180383
## 46: 0.002152081 -2.4868295 0.6511067 0.45180383
## 47: 0.004864501 -1.1164337 0.5523848 0.01618970
## 48: 0.004864501 -1.1164337 0.5523848 0.01618970
## 49: 0.004864501 -1.1164337 0.5523848 0.01618970
## 50: 0.004864501 -1.1164337 0.5523848 0.01618970
## 51: 0.004864501 -1.1164337 0.5523848 0.01618970
## 52: 0.004864501 -1.1164337 0.5523848 0.01618970
## 53: 0.004864501 -1.1164337 0.5523848 0.01618970
## 54: 0.004864501 -1.1164337 0.5523848 0.01618970
## 55: 0.003528384 -2.1142499 0.8366451 0.41090035
## 56: 0.003528384 -2.1142499 0.8366451 0.41090035
## 57: 0.003528384 -2.1142499 0.8366451 0.41090035
## 58: 0.005015553 -0.5818054 0.1606180 0.05815236
## 59: 0.005015553 -0.5818054 0.1606180 0.05815236
## 60: 0.005015553 -0.5818054 0.1606180 0.05815236
## 61: 0.005015553 -0.5818054 0.1606180 0.05815236
## 62: 0.005015553 -0.5818054 0.1606180 0.05815236
## 63: 0.005015553 -0.5818054 0.1606180 0.05815236
## 64: 0.005015553 -0.5818054 0.1606180 0.05815236
## 65: 0.005015553 -0.5818054 0.1606180 0.05815236
## 66: 0.005015553 -0.5818054 0.1606180 0.05815236
## 67: 0.005015553 -0.5818054 0.1606180 0.05815236
## 68: 0.005015553 -0.5818054 0.1606180 0.05815236
## 69: 0.005015553 -0.5818054 0.1606180 0.05815236
## 70: 0.005015553 -0.5818054 0.1606180 0.05815236
## 71: 0.005015553 -0.5818054 0.1606180 0.05815236
## 72: 0.005015553 -0.5818054 0.1606180 0.05815236
## 73: 0.005015553 -0.5818054 0.1606180 0.05815236
## 74: 0.005015553 -0.5818054 0.1606180 0.05815236
## 75: 0.005277323 -0.4880865 0.5526595 0.97974651
## 76: 0.005277323 -0.4880865 0.5526595 0.97974651
## se.bp v c pchi
## [1] "ORF25" "ORF35.5" "ORF58" "ORF50" "ORF64_1" "ORF42" "ORF33"
## [8] "ORF34" "ORF62" "ORF4" "ORF20" "ORF21" "ORF61" "ORF31"
## [15] "ORF1" "NOIR_1" "ORF32" "ORF59" "ORF69"## [1] 19## [1] "ORF12" "ORF13" "ORF15" "ORF16" "ORF27" "ORF32" "ORF35" "ORF41"
## [9] "ORF48" "ORF52" "ORF54" "ORF57" "ORF59" "ORF60" "NOIR_1" "ORF71"
## [17] "ORF72" "ORF69" "ORF70"## [1] 19Clustering statistics: Cluster number: 6
## Key: <cluster>
## cluster gene si au bp se.si se.au
## <int> <char> <num> <num> <num> <num> <num>
## 1: 1 ORF1 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 2: 1 ORF2 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 3: 1 ORF3 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 4: 1 ORF4 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 5: 1 ORF8 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 6: 1 ORF9 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 7: 1 ORF11 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 8: 1 ORF14 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 9: 1 ORF18 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 10: 1 ORF19 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 11: 1 ORF20 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 12: 1 ORF21 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 13: 1 ORF22 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 14: 1 ORF23 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 15: 1 ORF24 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 16: 1 ORF25 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 17: 1 ORF26 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 18: 1 ORF28 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 19: 1 ORF29 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 20: 1 ORF31 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 21: 1 ORF33 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 22: 1 ORF34 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 23: 1 ORF35.5 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 24: 1 ORF36 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 25: 1 ORF37 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 26: 1 ORF38 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 27: 1 ORF39 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 28: 1 CTO 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 29: 1 ORF40 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 30: 1 ORF42 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 31: 1 ORF43 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 32: 1 ORF44 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 33: 1 ORF46 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 34: 1 ORF49 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 35: 1 ORF50 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 36: 1 ORF51 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 37: 1 ORF58 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 38: 1 ORF61 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 39: 1 ORF62 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 40: 1 ORF64_1 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 41: 1 ORF66_1 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 42: 1 ORF68 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 43: 1 ORF73 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 44: 1 ORF74 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 45: 1 ORF75 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 46: 1 ORF76 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 47: 2 ORF5 0.8361360 0.9524233 0.7136396 0.019845119 0.0077877677
## 48: 2 ORF7 0.8361360 0.9524233 0.7136396 0.019845119 0.0077877677
## 49: 2 ORF10 0.8361360 0.9524233 0.7136396 0.019845119 0.0077877677
## 50: 2 ORF17 0.8361360 0.9524233 0.7136396 0.019845119 0.0077877677
## 51: 2 ORF30 0.8361360 0.9524233 0.7136396 0.019845119 0.0077877677
## 52: 2 ORF53 0.8361360 0.9524233 0.7136396 0.019845119 0.0077877677
## 53: 2 ORF63 0.8361360 0.9524233 0.7136396 0.019845119 0.0077877677
## 54: 2 NOIR_2 0.8361360 0.9524233 0.7136396 0.019845119 0.0077877677
## 55: 3 ORF6 0.9921335 0.9984157 0.8993056 0.002040977 0.0005060408
## 56: 3 ORF65_1 0.9921335 0.9984157 0.8993056 0.002040977 0.0005060408
## 57: 3 ORF67_1 0.9921335 0.9984157 0.8993056 0.002040977 0.0005060408
## 58: 4 ORF12 0.4752019 0.7710846 0.6631909 0.036465996 0.0232411811
## 59: 4 ORF13 0.4752019 0.7710846 0.6631909 0.036465996 0.0232411811
## 60: 4 ORF15 0.4752019 0.7710846 0.6631909 0.036465996 0.0232411811
## 61: 4 ORF16 0.4752019 0.7710846 0.6631909 0.036465996 0.0232411811
## 62: 4 ORF35 0.4752019 0.7710846 0.6631909 0.036465996 0.0232411811
## 63: 4 ORF41 0.4752019 0.7710846 0.6631909 0.036465996 0.0232411811
## 64: 4 ORF48 0.4752019 0.7710846 0.6631909 0.036465996 0.0232411811
## 65: 4 ORF52 0.4752019 0.7710846 0.6631909 0.036465996 0.0232411811
## 66: 4 ORF54 0.4752019 0.7710846 0.6631909 0.036465996 0.0232411811
## 67: 4 ORF57 0.4752019 0.7710846 0.6631909 0.036465996 0.0232411811
## 68: 4 ORF60 0.4752019 0.7710846 0.6631909 0.036465996 0.0232411811
## 69: 4 ORF71 0.4752019 0.7710846 0.6631909 0.036465996 0.0232411811
## 70: 4 ORF72 0.4752019 0.7710846 0.6631909 0.036465996 0.0232411811
## 71: 5 ORF27 0.4866577 0.8510033 0.4742570 0.039463824 0.0177067445
## 72: 5 ORF32 0.4866577 0.8510033 0.4742570 0.039463824 0.0177067445
## 73: 5 ORF59 0.4866577 0.8510033 0.4742570 0.039463824 0.0177067445
## 74: 5 NOIR_1 0.4866577 0.8510033 0.4742570 0.039463824 0.0177067445
## 75: 6 ORF69 0.7546193 0.9302651 0.6319019 0.025775455 0.0102798908
## 76: 6 ORF70 0.7546193 0.9302651 0.6319019 0.025775455 0.0102798908
## cluster gene si au bp se.si se.au
## se.bp v c pchi
## <num> <num> <num> <num>
## 1: 0.002152081 -2.4868295 0.6511067 0.45180383
## 2: 0.002152081 -2.4868295 0.6511067 0.45180383
## 3: 0.002152081 -2.4868295 0.6511067 0.45180383
## 4: 0.002152081 -2.4868295 0.6511067 0.45180383
## 5: 0.002152081 -2.4868295 0.6511067 0.45180383
## 6: 0.002152081 -2.4868295 0.6511067 0.45180383
## 7: 0.002152081 -2.4868295 0.6511067 0.45180383
## 8: 0.002152081 -2.4868295 0.6511067 0.45180383
## 9: 0.002152081 -2.4868295 0.6511067 0.45180383
## 10: 0.002152081 -2.4868295 0.6511067 0.45180383
## 11: 0.002152081 -2.4868295 0.6511067 0.45180383
## 12: 0.002152081 -2.4868295 0.6511067 0.45180383
## 13: 0.002152081 -2.4868295 0.6511067 0.45180383
## 14: 0.002152081 -2.4868295 0.6511067 0.45180383
## 15: 0.002152081 -2.4868295 0.6511067 0.45180383
## 16: 0.002152081 -2.4868295 0.6511067 0.45180383
## 17: 0.002152081 -2.4868295 0.6511067 0.45180383
## 18: 0.002152081 -2.4868295 0.6511067 0.45180383
## 19: 0.002152081 -2.4868295 0.6511067 0.45180383
## 20: 0.002152081 -2.4868295 0.6511067 0.45180383
## 21: 0.002152081 -2.4868295 0.6511067 0.45180383
## 22: 0.002152081 -2.4868295 0.6511067 0.45180383
## 23: 0.002152081 -2.4868295 0.6511067 0.45180383
## 24: 0.002152081 -2.4868295 0.6511067 0.45180383
## 25: 0.002152081 -2.4868295 0.6511067 0.45180383
## 26: 0.002152081 -2.4868295 0.6511067 0.45180383
## 27: 0.002152081 -2.4868295 0.6511067 0.45180383
## 28: 0.002152081 -2.4868295 0.6511067 0.45180383
## 29: 0.002152081 -2.4868295 0.6511067 0.45180383
## 30: 0.002152081 -2.4868295 0.6511067 0.45180383
## 31: 0.002152081 -2.4868295 0.6511067 0.45180383
## 32: 0.002152081 -2.4868295 0.6511067 0.45180383
## 33: 0.002152081 -2.4868295 0.6511067 0.45180383
## 34: 0.002152081 -2.4868295 0.6511067 0.45180383
## 35: 0.002152081 -2.4868295 0.6511067 0.45180383
## 36: 0.002152081 -2.4868295 0.6511067 0.45180383
## 37: 0.002152081 -2.4868295 0.6511067 0.45180383
## 38: 0.002152081 -2.4868295 0.6511067 0.45180383
## 39: 0.002152081 -2.4868295 0.6511067 0.45180383
## 40: 0.002152081 -2.4868295 0.6511067 0.45180383
## 41: 0.002152081 -2.4868295 0.6511067 0.45180383
## 42: 0.002152081 -2.4868295 0.6511067 0.45180383
## 43: 0.002152081 -2.4868295 0.6511067 0.45180383
## 44: 0.002152081 -2.4868295 0.6511067 0.45180383
## 45: 0.002152081 -2.4868295 0.6511067 0.45180383
## 46: 0.002152081 -2.4868295 0.6511067 0.45180383
## 47: 0.004864501 -1.1164337 0.5523848 0.01618970
## 48: 0.004864501 -1.1164337 0.5523848 0.01618970
## 49: 0.004864501 -1.1164337 0.5523848 0.01618970
## 50: 0.004864501 -1.1164337 0.5523848 0.01618970
## 51: 0.004864501 -1.1164337 0.5523848 0.01618970
## 52: 0.004864501 -1.1164337 0.5523848 0.01618970
## 53: 0.004864501 -1.1164337 0.5523848 0.01618970
## 54: 0.004864501 -1.1164337 0.5523848 0.01618970
## 55: 0.003528384 -2.1142499 0.8366451 0.41090035
## 56: 0.003528384 -2.1142499 0.8366451 0.41090035
## 57: 0.003528384 -2.1142499 0.8366451 0.41090035
## 58: 0.005015553 -0.5818054 0.1606180 0.05815236
## 59: 0.005015553 -0.5818054 0.1606180 0.05815236
## 60: 0.005015553 -0.5818054 0.1606180 0.05815236
## 61: 0.005015553 -0.5818054 0.1606180 0.05815236
## 62: 0.005015553 -0.5818054 0.1606180 0.05815236
## 63: 0.005015553 -0.5818054 0.1606180 0.05815236
## 64: 0.005015553 -0.5818054 0.1606180 0.05815236
## 65: 0.005015553 -0.5818054 0.1606180 0.05815236
## 66: 0.005015553 -0.5818054 0.1606180 0.05815236
## 67: 0.005015553 -0.5818054 0.1606180 0.05815236
## 68: 0.005015553 -0.5818054 0.1606180 0.05815236
## 69: 0.005015553 -0.5818054 0.1606180 0.05815236
## 70: 0.005015553 -0.5818054 0.1606180 0.05815236
## 71: 0.005277323 -0.4880865 0.5526595 0.97974651
## 72: 0.005277323 -0.4880865 0.5526595 0.97974651
## 73: 0.005277323 -0.4880865 0.5526595 0.97974651
## 74: 0.005277323 -0.4880865 0.5526595 0.97974651
## 75: 0.005155700 -0.9073314 0.5704366 0.48841392
## 76: 0.005155700 -0.9073314 0.5704366 0.48841392
## se.bp v c pchi
## [1] "ORF43" "ORF44" "ORF25" "ORF50" "ORF64_1" "ORF35.5" "ORF58"
## [8] "ORF34" "ORF4" "ORF42" "ORF33" "ORF20" "ORF21" "ORF61"
## [15] "ORF62" "ORF31" "ORF1" "ORF69"## [1] 18## [1] "ORF12" "ORF13" "ORF15" "ORF16" "ORF35" "ORF41" "ORF48" "ORF52"
## [9] "ORF54" "ORF57" "ORF60" "ORF71" "ORF72" "ORF27" "ORF32" "ORF59"
## [17] "NOIR_1" "ORF69" "ORF70"## [1] 19Clustering statistics: Cluster number: 7
## Key: <cluster>
## cluster gene si au bp se.si se.au
## <int> <char> <num> <num> <num> <num> <num>
## 1: 1 ORF1 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 2: 1 ORF4 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 3: 1 ORF9 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 4: 1 ORF19 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 5: 1 ORF20 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 6: 1 ORF21 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 7: 1 ORF31 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 8: 1 ORF34 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 9: 1 ORF37 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 10: 1 ORF38 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 11: 1 ORF49 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 12: 1 ORF50 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 13: 1 ORF51 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 14: 1 ORF61 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 15: 1 ORF64_1 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 16: 2 ORF2 0.8361360 0.9524233 0.7136396 0.019845119 0.0077877677
## 17: 2 ORF3 0.8361360 0.9524233 0.7136396 0.019845119 0.0077877677
## 18: 2 ORF8 0.8361360 0.9524233 0.7136396 0.019845119 0.0077877677
## 19: 2 ORF11 0.8361360 0.9524233 0.7136396 0.019845119 0.0077877677
## 20: 2 ORF14 0.8361360 0.9524233 0.7136396 0.019845119 0.0077877677
## 21: 2 ORF18 0.8361360 0.9524233 0.7136396 0.019845119 0.0077877677
## 22: 2 ORF22 0.8361360 0.9524233 0.7136396 0.019845119 0.0077877677
## 23: 2 ORF23 0.8361360 0.9524233 0.7136396 0.019845119 0.0077877677
## 24: 2 ORF24 0.8361360 0.9524233 0.7136396 0.019845119 0.0077877677
## 25: 2 ORF25 0.8361360 0.9524233 0.7136396 0.019845119 0.0077877677
## 26: 2 ORF26 0.8361360 0.9524233 0.7136396 0.019845119 0.0077877677
## 27: 2 ORF28 0.8361360 0.9524233 0.7136396 0.019845119 0.0077877677
## 28: 2 ORF29 0.8361360 0.9524233 0.7136396 0.019845119 0.0077877677
## 29: 2 ORF33 0.8361360 0.9524233 0.7136396 0.019845119 0.0077877677
## 30: 2 ORF35.5 0.8361360 0.9524233 0.7136396 0.019845119 0.0077877677
## 31: 2 ORF36 0.8361360 0.9524233 0.7136396 0.019845119 0.0077877677
## 32: 2 ORF39 0.8361360 0.9524233 0.7136396 0.019845119 0.0077877677
## 33: 2 CTO 0.8361360 0.9524233 0.7136396 0.019845119 0.0077877677
## 34: 2 ORF40 0.8361360 0.9524233 0.7136396 0.019845119 0.0077877677
## 35: 2 ORF42 0.8361360 0.9524233 0.7136396 0.019845119 0.0077877677
## 36: 2 ORF43 0.8361360 0.9524233 0.7136396 0.019845119 0.0077877677
## 37: 2 ORF44 0.8361360 0.9524233 0.7136396 0.019845119 0.0077877677
## 38: 2 ORF46 0.8361360 0.9524233 0.7136396 0.019845119 0.0077877677
## 39: 2 ORF58 0.8361360 0.9524233 0.7136396 0.019845119 0.0077877677
## 40: 2 ORF62 0.8361360 0.9524233 0.7136396 0.019845119 0.0077877677
## 41: 2 ORF66_1 0.8361360 0.9524233 0.7136396 0.019845119 0.0077877677
## 42: 2 ORF68 0.8361360 0.9524233 0.7136396 0.019845119 0.0077877677
## 43: 2 ORF73 0.8361360 0.9524233 0.7136396 0.019845119 0.0077877677
## 44: 2 ORF74 0.8361360 0.9524233 0.7136396 0.019845119 0.0077877677
## 45: 2 ORF75 0.8361360 0.9524233 0.7136396 0.019845119 0.0077877677
## 46: 2 ORF76 0.8361360 0.9524233 0.7136396 0.019845119 0.0077877677
## 47: 3 ORF5 0.9921335 0.9984157 0.8993056 0.002040977 0.0005060408
## 48: 3 ORF7 0.9921335 0.9984157 0.8993056 0.002040977 0.0005060408
## 49: 3 ORF10 0.9921335 0.9984157 0.8993056 0.002040977 0.0005060408
## 50: 3 ORF17 0.9921335 0.9984157 0.8993056 0.002040977 0.0005060408
## 51: 3 ORF30 0.9921335 0.9984157 0.8993056 0.002040977 0.0005060408
## 52: 3 ORF53 0.9921335 0.9984157 0.8993056 0.002040977 0.0005060408
## 53: 3 ORF63 0.9921335 0.9984157 0.8993056 0.002040977 0.0005060408
## 54: 3 NOIR_2 0.9921335 0.9984157 0.8993056 0.002040977 0.0005060408
## 55: 4 ORF6 0.4752019 0.7710846 0.6631909 0.036465996 0.0232411811
## 56: 4 ORF65_1 0.4752019 0.7710846 0.6631909 0.036465996 0.0232411811
## 57: 4 ORF67_1 0.4752019 0.7710846 0.6631909 0.036465996 0.0232411811
## 58: 5 ORF12 0.4866577 0.8510033 0.4742570 0.039463824 0.0177067445
## 59: 5 ORF13 0.4866577 0.8510033 0.4742570 0.039463824 0.0177067445
## 60: 5 ORF15 0.4866577 0.8510033 0.4742570 0.039463824 0.0177067445
## 61: 5 ORF16 0.4866577 0.8510033 0.4742570 0.039463824 0.0177067445
## 62: 5 ORF35 0.4866577 0.8510033 0.4742570 0.039463824 0.0177067445
## 63: 5 ORF41 0.4866577 0.8510033 0.4742570 0.039463824 0.0177067445
## 64: 5 ORF48 0.4866577 0.8510033 0.4742570 0.039463824 0.0177067445
## 65: 5 ORF52 0.4866577 0.8510033 0.4742570 0.039463824 0.0177067445
## 66: 5 ORF54 0.4866577 0.8510033 0.4742570 0.039463824 0.0177067445
## 67: 5 ORF57 0.4866577 0.8510033 0.4742570 0.039463824 0.0177067445
## 68: 5 ORF60 0.4866577 0.8510033 0.4742570 0.039463824 0.0177067445
## 69: 5 ORF71 0.4866577 0.8510033 0.4742570 0.039463824 0.0177067445
## 70: 5 ORF72 0.4866577 0.8510033 0.4742570 0.039463824 0.0177067445
## 71: 6 ORF27 0.7546193 0.9302651 0.6319019 0.025775455 0.0102798908
## 72: 6 ORF32 0.7546193 0.9302651 0.6319019 0.025775455 0.0102798908
## 73: 6 ORF59 0.7546193 0.9302651 0.6319019 0.025775455 0.0102798908
## 74: 6 NOIR_1 0.7546193 0.9302651 0.6319019 0.025775455 0.0102798908
## 75: 7 ORF69 0.8499612 0.9623404 0.6685152 0.018635343 0.0063920360
## 76: 7 ORF70 0.8499612 0.9623404 0.6685152 0.018635343 0.0063920360
## cluster gene si au bp se.si se.au
## se.bp v c pchi
## <num> <num> <num> <num>
## 1: 0.002152081 -2.4868295 0.6511067 0.45180383
## 2: 0.002152081 -2.4868295 0.6511067 0.45180383
## 3: 0.002152081 -2.4868295 0.6511067 0.45180383
## 4: 0.002152081 -2.4868295 0.6511067 0.45180383
## 5: 0.002152081 -2.4868295 0.6511067 0.45180383
## 6: 0.002152081 -2.4868295 0.6511067 0.45180383
## 7: 0.002152081 -2.4868295 0.6511067 0.45180383
## 8: 0.002152081 -2.4868295 0.6511067 0.45180383
## 9: 0.002152081 -2.4868295 0.6511067 0.45180383
## 10: 0.002152081 -2.4868295 0.6511067 0.45180383
## 11: 0.002152081 -2.4868295 0.6511067 0.45180383
## 12: 0.002152081 -2.4868295 0.6511067 0.45180383
## 13: 0.002152081 -2.4868295 0.6511067 0.45180383
## 14: 0.002152081 -2.4868295 0.6511067 0.45180383
## 15: 0.002152081 -2.4868295 0.6511067 0.45180383
## 16: 0.004864501 -1.1164337 0.5523848 0.01618970
## 17: 0.004864501 -1.1164337 0.5523848 0.01618970
## 18: 0.004864501 -1.1164337 0.5523848 0.01618970
## 19: 0.004864501 -1.1164337 0.5523848 0.01618970
## 20: 0.004864501 -1.1164337 0.5523848 0.01618970
## 21: 0.004864501 -1.1164337 0.5523848 0.01618970
## 22: 0.004864501 -1.1164337 0.5523848 0.01618970
## 23: 0.004864501 -1.1164337 0.5523848 0.01618970
## 24: 0.004864501 -1.1164337 0.5523848 0.01618970
## 25: 0.004864501 -1.1164337 0.5523848 0.01618970
## 26: 0.004864501 -1.1164337 0.5523848 0.01618970
## 27: 0.004864501 -1.1164337 0.5523848 0.01618970
## 28: 0.004864501 -1.1164337 0.5523848 0.01618970
## 29: 0.004864501 -1.1164337 0.5523848 0.01618970
## 30: 0.004864501 -1.1164337 0.5523848 0.01618970
## 31: 0.004864501 -1.1164337 0.5523848 0.01618970
## 32: 0.004864501 -1.1164337 0.5523848 0.01618970
## 33: 0.004864501 -1.1164337 0.5523848 0.01618970
## 34: 0.004864501 -1.1164337 0.5523848 0.01618970
## 35: 0.004864501 -1.1164337 0.5523848 0.01618970
## 36: 0.004864501 -1.1164337 0.5523848 0.01618970
## 37: 0.004864501 -1.1164337 0.5523848 0.01618970
## 38: 0.004864501 -1.1164337 0.5523848 0.01618970
## 39: 0.004864501 -1.1164337 0.5523848 0.01618970
## 40: 0.004864501 -1.1164337 0.5523848 0.01618970
## 41: 0.004864501 -1.1164337 0.5523848 0.01618970
## 42: 0.004864501 -1.1164337 0.5523848 0.01618970
## 43: 0.004864501 -1.1164337 0.5523848 0.01618970
## 44: 0.004864501 -1.1164337 0.5523848 0.01618970
## 45: 0.004864501 -1.1164337 0.5523848 0.01618970
## 46: 0.004864501 -1.1164337 0.5523848 0.01618970
## 47: 0.003528384 -2.1142499 0.8366451 0.41090035
## 48: 0.003528384 -2.1142499 0.8366451 0.41090035
## 49: 0.003528384 -2.1142499 0.8366451 0.41090035
## 50: 0.003528384 -2.1142499 0.8366451 0.41090035
## 51: 0.003528384 -2.1142499 0.8366451 0.41090035
## 52: 0.003528384 -2.1142499 0.8366451 0.41090035
## 53: 0.003528384 -2.1142499 0.8366451 0.41090035
## 54: 0.003528384 -2.1142499 0.8366451 0.41090035
## 55: 0.005015553 -0.5818054 0.1606180 0.05815236
## 56: 0.005015553 -0.5818054 0.1606180 0.05815236
## 57: 0.005015553 -0.5818054 0.1606180 0.05815236
## 58: 0.005277323 -0.4880865 0.5526595 0.97974651
## 59: 0.005277323 -0.4880865 0.5526595 0.97974651
## 60: 0.005277323 -0.4880865 0.5526595 0.97974651
## 61: 0.005277323 -0.4880865 0.5526595 0.97974651
## 62: 0.005277323 -0.4880865 0.5526595 0.97974651
## 63: 0.005277323 -0.4880865 0.5526595 0.97974651
## 64: 0.005277323 -0.4880865 0.5526595 0.97974651
## 65: 0.005277323 -0.4880865 0.5526595 0.97974651
## 66: 0.005277323 -0.4880865 0.5526595 0.97974651
## 67: 0.005277323 -0.4880865 0.5526595 0.97974651
## 68: 0.005277323 -0.4880865 0.5526595 0.97974651
## 69: 0.005277323 -0.4880865 0.5526595 0.97974651
## 70: 0.005277323 -0.4880865 0.5526595 0.97974651
## 71: 0.005155700 -0.9073314 0.5704366 0.48841392
## 72: 0.005155700 -0.9073314 0.5704366 0.48841392
## 73: 0.005155700 -0.9073314 0.5704366 0.48841392
## 74: 0.005155700 -0.9073314 0.5704366 0.48841392
## 75: 0.005076291 -1.1071663 0.6713495 0.96807380
## 76: 0.005076291 -1.1071663 0.6713495 0.96807380
## se.bp v c pchi
## [1] "ORF61" "ORF21" "ORF19" "ORF49" "ORF31" "ORF1" "ORF42" "ORF18" "ORF33"
## [10] "ORF62" "ORF69"## [1] 11## [1] "ORF6" "ORF65_1" "ORF67_1" "ORF12" "ORF13" "ORF15" "ORF16"
## [8] "ORF35" "ORF41" "ORF48" "ORF52" "ORF54" "ORF57" "ORF60"
## [15] "ORF71" "ORF72" "ORF27" "ORF32" "ORF59" "NOIR_1"## [1] 20Clustering statistics: Cluster number: 10
## Key: <cluster>
## cluster gene si au bp se.si se.au
## <int> <char> <num> <num> <num> <num> <num>
## 1: 1 ORF1 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 2: 1 ORF4 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 3: 1 ORF9 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 4: 1 ORF20 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 5: 1 ORF21 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 6: 1 ORF31 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 7: 1 ORF34 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 8: 1 ORF38 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 9: 1 ORF50 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 10: 1 ORF61 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 11: 1 ORF64_1 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 12: 2 ORF2 0.8361360 0.9524233 0.7136396 0.019845119 0.0077877677
## 13: 2 ORF3 0.8361360 0.9524233 0.7136396 0.019845119 0.0077877677
## 14: 2 ORF11 0.8361360 0.9524233 0.7136396 0.019845119 0.0077877677
## 15: 2 ORF14 0.8361360 0.9524233 0.7136396 0.019845119 0.0077877677
## 16: 2 ORF18 0.8361360 0.9524233 0.7136396 0.019845119 0.0077877677
## 17: 2 ORF26 0.8361360 0.9524233 0.7136396 0.019845119 0.0077877677
## 18: 2 ORF28 0.8361360 0.9524233 0.7136396 0.019845119 0.0077877677
## 19: 2 ORF29 0.8361360 0.9524233 0.7136396 0.019845119 0.0077877677
## 20: 2 ORF39 0.8361360 0.9524233 0.7136396 0.019845119 0.0077877677
## 21: 2 ORF40 0.8361360 0.9524233 0.7136396 0.019845119 0.0077877677
## 22: 2 ORF66_1 0.8361360 0.9524233 0.7136396 0.019845119 0.0077877677
## 23: 2 ORF73 0.8361360 0.9524233 0.7136396 0.019845119 0.0077877677
## 24: 2 ORF75 0.8361360 0.9524233 0.7136396 0.019845119 0.0077877677
## 25: 2 ORF76 0.8361360 0.9524233 0.7136396 0.019845119 0.0077877677
## 26: 3 ORF5 0.9921335 0.9984157 0.8993056 0.002040977 0.0005060408
## 27: 3 ORF7 0.9921335 0.9984157 0.8993056 0.002040977 0.0005060408
## 28: 3 ORF10 0.9921335 0.9984157 0.8993056 0.002040977 0.0005060408
## 29: 3 ORF17 0.9921335 0.9984157 0.8993056 0.002040977 0.0005060408
## 30: 3 ORF30 0.9921335 0.9984157 0.8993056 0.002040977 0.0005060408
## 31: 3 ORF53 0.9921335 0.9984157 0.8993056 0.002040977 0.0005060408
## 32: 3 ORF63 0.9921335 0.9984157 0.8993056 0.002040977 0.0005060408
## 33: 3 NOIR_2 0.9921335 0.9984157 0.8993056 0.002040977 0.0005060408
## 34: 4 ORF6 0.4752019 0.7710846 0.6631909 0.036465996 0.0232411811
## 35: 4 ORF65_1 0.4752019 0.7710846 0.6631909 0.036465996 0.0232411811
## 36: 4 ORF67_1 0.4752019 0.7710846 0.6631909 0.036465996 0.0232411811
## 37: 5 ORF8 0.4866577 0.8510033 0.4742570 0.039463824 0.0177067445
## 38: 5 ORF22 0.4866577 0.8510033 0.4742570 0.039463824 0.0177067445
## 39: 5 ORF23 0.4866577 0.8510033 0.4742570 0.039463824 0.0177067445
## 40: 5 ORF25 0.4866577 0.8510033 0.4742570 0.039463824 0.0177067445
## 41: 5 ORF33 0.4866577 0.8510033 0.4742570 0.039463824 0.0177067445
## 42: 5 ORF35.5 0.4866577 0.8510033 0.4742570 0.039463824 0.0177067445
## 43: 5 ORF36 0.4866577 0.8510033 0.4742570 0.039463824 0.0177067445
## 44: 5 CTO 0.4866577 0.8510033 0.4742570 0.039463824 0.0177067445
## 45: 5 ORF42 0.4866577 0.8510033 0.4742570 0.039463824 0.0177067445
## 46: 5 ORF43 0.4866577 0.8510033 0.4742570 0.039463824 0.0177067445
## 47: 5 ORF44 0.4866577 0.8510033 0.4742570 0.039463824 0.0177067445
## 48: 5 ORF46 0.4866577 0.8510033 0.4742570 0.039463824 0.0177067445
## 49: 5 ORF58 0.4866577 0.8510033 0.4742570 0.039463824 0.0177067445
## 50: 5 ORF62 0.4866577 0.8510033 0.4742570 0.039463824 0.0177067445
## 51: 6 ORF12 0.7546193 0.9302651 0.6319019 0.025775455 0.0102798908
## 52: 6 ORF13 0.7546193 0.9302651 0.6319019 0.025775455 0.0102798908
## 53: 6 ORF15 0.7546193 0.9302651 0.6319019 0.025775455 0.0102798908
## 54: 6 ORF16 0.7546193 0.9302651 0.6319019 0.025775455 0.0102798908
## 55: 6 ORF35 0.7546193 0.9302651 0.6319019 0.025775455 0.0102798908
## 56: 6 ORF41 0.7546193 0.9302651 0.6319019 0.025775455 0.0102798908
## 57: 6 ORF48 0.7546193 0.9302651 0.6319019 0.025775455 0.0102798908
## 58: 6 ORF52 0.7546193 0.9302651 0.6319019 0.025775455 0.0102798908
## 59: 6 ORF54 0.7546193 0.9302651 0.6319019 0.025775455 0.0102798908
## 60: 6 ORF57 0.7546193 0.9302651 0.6319019 0.025775455 0.0102798908
## 61: 6 ORF60 0.7546193 0.9302651 0.6319019 0.025775455 0.0102798908
## 62: 6 ORF71 0.7546193 0.9302651 0.6319019 0.025775455 0.0102798908
## 63: 6 ORF72 0.7546193 0.9302651 0.6319019 0.025775455 0.0102798908
## 64: 7 ORF19 0.8499612 0.9623404 0.6685152 0.018635343 0.0063920360
## 65: 7 ORF37 0.8499612 0.9623404 0.6685152 0.018635343 0.0063920360
## 66: 7 ORF49 0.8499612 0.9623404 0.6685152 0.018635343 0.0063920360
## 67: 7 ORF51 0.8499612 0.9623404 0.6685152 0.018635343 0.0063920360
## 68: 8 ORF24 0.9948989 0.9992090 0.8706208 0.001303207 0.0002516741
## 69: 8 ORF68 0.9948989 0.9992090 0.8706208 0.001303207 0.0002516741
## 70: 8 ORF74 0.9948989 0.9992090 0.8706208 0.001303207 0.0002516741
## 71: 9 ORF27 0.8452656 0.9779106 0.4508009 0.020208903 0.0041959358
## 72: 9 ORF32 0.8452656 0.9779106 0.4508009 0.020208903 0.0041959358
## 73: 9 ORF59 0.8452656 0.9779106 0.4508009 0.020208903 0.0041959358
## 74: 9 NOIR_1 0.8452656 0.9779106 0.4508009 0.020208903 0.0041959358
## 75: 10 ORF69 0.8521517 0.9860876 0.3328321 0.021534613 0.0030460671
## 76: 10 ORF70 0.8521517 0.9860876 0.3328321 0.021534613 0.0030460671
## cluster gene si au bp se.si se.au
## se.bp v c pchi
## <num> <num> <num> <num>
## 1: 0.002152081 -2.4868295 0.6511067 0.45180383
## 2: 0.002152081 -2.4868295 0.6511067 0.45180383
## 3: 0.002152081 -2.4868295 0.6511067 0.45180383
## 4: 0.002152081 -2.4868295 0.6511067 0.45180383
## 5: 0.002152081 -2.4868295 0.6511067 0.45180383
## 6: 0.002152081 -2.4868295 0.6511067 0.45180383
## 7: 0.002152081 -2.4868295 0.6511067 0.45180383
## 8: 0.002152081 -2.4868295 0.6511067 0.45180383
## 9: 0.002152081 -2.4868295 0.6511067 0.45180383
## 10: 0.002152081 -2.4868295 0.6511067 0.45180383
## 11: 0.002152081 -2.4868295 0.6511067 0.45180383
## 12: 0.004864501 -1.1164337 0.5523848 0.01618970
## 13: 0.004864501 -1.1164337 0.5523848 0.01618970
## 14: 0.004864501 -1.1164337 0.5523848 0.01618970
## 15: 0.004864501 -1.1164337 0.5523848 0.01618970
## 16: 0.004864501 -1.1164337 0.5523848 0.01618970
## 17: 0.004864501 -1.1164337 0.5523848 0.01618970
## 18: 0.004864501 -1.1164337 0.5523848 0.01618970
## 19: 0.004864501 -1.1164337 0.5523848 0.01618970
## 20: 0.004864501 -1.1164337 0.5523848 0.01618970
## 21: 0.004864501 -1.1164337 0.5523848 0.01618970
## 22: 0.004864501 -1.1164337 0.5523848 0.01618970
## 23: 0.004864501 -1.1164337 0.5523848 0.01618970
## 24: 0.004864501 -1.1164337 0.5523848 0.01618970
## 25: 0.004864501 -1.1164337 0.5523848 0.01618970
## 26: 0.003528384 -2.1142499 0.8366451 0.41090035
## 27: 0.003528384 -2.1142499 0.8366451 0.41090035
## 28: 0.003528384 -2.1142499 0.8366451 0.41090035
## 29: 0.003528384 -2.1142499 0.8366451 0.41090035
## 30: 0.003528384 -2.1142499 0.8366451 0.41090035
## 31: 0.003528384 -2.1142499 0.8366451 0.41090035
## 32: 0.003528384 -2.1142499 0.8366451 0.41090035
## 33: 0.003528384 -2.1142499 0.8366451 0.41090035
## 34: 0.005015553 -0.5818054 0.1606180 0.05815236
## 35: 0.005015553 -0.5818054 0.1606180 0.05815236
## 36: 0.005015553 -0.5818054 0.1606180 0.05815236
## 37: 0.005277323 -0.4880865 0.5526595 0.97974651
## 38: 0.005277323 -0.4880865 0.5526595 0.97974651
## 39: 0.005277323 -0.4880865 0.5526595 0.97974651
## 40: 0.005277323 -0.4880865 0.5526595 0.97974651
## 41: 0.005277323 -0.4880865 0.5526595 0.97974651
## 42: 0.005277323 -0.4880865 0.5526595 0.97974651
## 43: 0.005277323 -0.4880865 0.5526595 0.97974651
## 44: 0.005277323 -0.4880865 0.5526595 0.97974651
## 45: 0.005277323 -0.4880865 0.5526595 0.97974651
## 46: 0.005277323 -0.4880865 0.5526595 0.97974651
## 47: 0.005277323 -0.4880865 0.5526595 0.97974651
## 48: 0.005277323 -0.4880865 0.5526595 0.97974651
## 49: 0.005277323 -0.4880865 0.5526595 0.97974651
## 50: 0.005277323 -0.4880865 0.5526595 0.97974651
## 51: 0.005155700 -0.9073314 0.5704366 0.48841392
## 52: 0.005155700 -0.9073314 0.5704366 0.48841392
## 53: 0.005155700 -0.9073314 0.5704366 0.48841392
## 54: 0.005155700 -0.9073314 0.5704366 0.48841392
## 55: 0.005155700 -0.9073314 0.5704366 0.48841392
## 56: 0.005155700 -0.9073314 0.5704366 0.48841392
## 57: 0.005155700 -0.9073314 0.5704366 0.48841392
## 58: 0.005155700 -0.9073314 0.5704366 0.48841392
## 59: 0.005155700 -0.9073314 0.5704366 0.48841392
## 60: 0.005155700 -0.9073314 0.5704366 0.48841392
## 61: 0.005155700 -0.9073314 0.5704366 0.48841392
## 62: 0.005155700 -0.9073314 0.5704366 0.48841392
## 63: 0.005155700 -0.9073314 0.5704366 0.48841392
## 64: 0.005076291 -1.1071663 0.6713495 0.96807380
## 65: 0.005076291 -1.1071663 0.6713495 0.96807380
## 66: 0.005076291 -1.1071663 0.6713495 0.96807380
## 67: 0.005076291 -1.1071663 0.6713495 0.96807380
## 68: 0.003885549 -2.1442641 1.0149336 0.03185429
## 69: 0.003885549 -2.1442641 1.0149336 0.03185429
## 70: 0.003885549 -2.1442641 1.0149336 0.03185429
## 71: 0.005295012 -0.9443758 1.0680139 0.40394260
## 72: 0.005295012 -0.9443758 1.0680139 0.40394260
## 73: 0.005295012 -0.9443758 1.0680139 0.40394260
## 74: 0.005295012 -0.9443758 1.0680139 0.40394260
## 75: 0.004996046 -0.8838204 1.3159266 0.26244569
## 76: 0.004996046 -0.8838204 1.3159266 0.26244569
## se.bp v c pchi
## [1] "ORF1" "ORF48" "ORF19" "ORF49" "ORF69"## [1] 5## [1] "ORF6" "ORF65_1" "ORF67_1" "ORF8" "ORF22" "ORF23" "ORF25"
## [8] "ORF33" "ORF35.5" "ORF36" "CTO" "ORF42" "ORF43" "ORF44"
## [15] "ORF46" "ORF58" "ORF62" "ORF12" "ORF13" "ORF15" "ORF16"
## [22] "ORF35" "ORF41" "ORF48" "ORF52" "ORF54" "ORF57" "ORF60"
## [29] "ORF71" "ORF72"## [1] 30Clustering statistics: Cluster number: 12
## Key: <cluster>
## cluster gene si au bp se.si se.au
## <int> <char> <num> <num> <num> <num> <num>
## 1: 1 ORF1 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 2: 1 ORF4 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 3: 1 ORF9 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 4: 1 ORF20 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 5: 1 ORF21 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 6: 1 ORF31 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 7: 1 ORF34 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 8: 1 ORF38 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 9: 1 ORF50 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 10: 1 ORF61 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 11: 2 ORF2 0.8361360 0.9524233 0.7136396 0.019845119 0.0077877677
## 12: 2 ORF3 0.8361360 0.9524233 0.7136396 0.019845119 0.0077877677
## 13: 2 ORF11 0.8361360 0.9524233 0.7136396 0.019845119 0.0077877677
## 14: 2 ORF14 0.8361360 0.9524233 0.7136396 0.019845119 0.0077877677
## 15: 2 ORF18 0.8361360 0.9524233 0.7136396 0.019845119 0.0077877677
## 16: 2 ORF26 0.8361360 0.9524233 0.7136396 0.019845119 0.0077877677
## 17: 2 ORF28 0.8361360 0.9524233 0.7136396 0.019845119 0.0077877677
## 18: 2 ORF29 0.8361360 0.9524233 0.7136396 0.019845119 0.0077877677
## 19: 2 ORF39 0.8361360 0.9524233 0.7136396 0.019845119 0.0077877677
## 20: 2 ORF40 0.8361360 0.9524233 0.7136396 0.019845119 0.0077877677
## 21: 2 ORF66_1 0.8361360 0.9524233 0.7136396 0.019845119 0.0077877677
## 22: 2 ORF73 0.8361360 0.9524233 0.7136396 0.019845119 0.0077877677
## 23: 2 ORF75 0.8361360 0.9524233 0.7136396 0.019845119 0.0077877677
## 24: 2 ORF76 0.8361360 0.9524233 0.7136396 0.019845119 0.0077877677
## 25: 3 ORF5 0.9921335 0.9984157 0.8993056 0.002040977 0.0005060408
## 26: 3 ORF7 0.9921335 0.9984157 0.8993056 0.002040977 0.0005060408
## 27: 3 ORF10 0.9921335 0.9984157 0.8993056 0.002040977 0.0005060408
## 28: 3 ORF17 0.9921335 0.9984157 0.8993056 0.002040977 0.0005060408
## 29: 3 ORF30 0.9921335 0.9984157 0.8993056 0.002040977 0.0005060408
## 30: 3 ORF53 0.9921335 0.9984157 0.8993056 0.002040977 0.0005060408
## 31: 3 ORF63 0.9921335 0.9984157 0.8993056 0.002040977 0.0005060408
## 32: 3 NOIR_2 0.9921335 0.9984157 0.8993056 0.002040977 0.0005060408
## 33: 4 ORF6 0.4752019 0.7710846 0.6631909 0.036465996 0.0232411811
## 34: 4 ORF65_1 0.4752019 0.7710846 0.6631909 0.036465996 0.0232411811
## 35: 4 ORF67_1 0.4752019 0.7710846 0.6631909 0.036465996 0.0232411811
## 36: 5 ORF8 0.4866577 0.8510033 0.4742570 0.039463824 0.0177067445
## 37: 5 ORF22 0.4866577 0.8510033 0.4742570 0.039463824 0.0177067445
## 38: 5 ORF23 0.4866577 0.8510033 0.4742570 0.039463824 0.0177067445
## 39: 5 ORF25 0.4866577 0.8510033 0.4742570 0.039463824 0.0177067445
## 40: 5 ORF33 0.4866577 0.8510033 0.4742570 0.039463824 0.0177067445
## 41: 5 ORF35.5 0.4866577 0.8510033 0.4742570 0.039463824 0.0177067445
## 42: 5 ORF36 0.4866577 0.8510033 0.4742570 0.039463824 0.0177067445
## 43: 5 CTO 0.4866577 0.8510033 0.4742570 0.039463824 0.0177067445
## 44: 5 ORF42 0.4866577 0.8510033 0.4742570 0.039463824 0.0177067445
## 45: 5 ORF43 0.4866577 0.8510033 0.4742570 0.039463824 0.0177067445
## 46: 5 ORF44 0.4866577 0.8510033 0.4742570 0.039463824 0.0177067445
## 47: 5 ORF46 0.4866577 0.8510033 0.4742570 0.039463824 0.0177067445
## 48: 5 ORF58 0.4866577 0.8510033 0.4742570 0.039463824 0.0177067445
## 49: 5 ORF62 0.4866577 0.8510033 0.4742570 0.039463824 0.0177067445
## 50: 6 ORF12 0.7546193 0.9302651 0.6319019 0.025775455 0.0102798908
## 51: 6 ORF13 0.7546193 0.9302651 0.6319019 0.025775455 0.0102798908
## 52: 6 ORF15 0.7546193 0.9302651 0.6319019 0.025775455 0.0102798908
## 53: 6 ORF16 0.7546193 0.9302651 0.6319019 0.025775455 0.0102798908
## 54: 6 ORF35 0.7546193 0.9302651 0.6319019 0.025775455 0.0102798908
## 55: 6 ORF41 0.7546193 0.9302651 0.6319019 0.025775455 0.0102798908
## 56: 6 ORF48 0.7546193 0.9302651 0.6319019 0.025775455 0.0102798908
## 57: 6 ORF52 0.7546193 0.9302651 0.6319019 0.025775455 0.0102798908
## 58: 6 ORF54 0.7546193 0.9302651 0.6319019 0.025775455 0.0102798908
## 59: 6 ORF57 0.7546193 0.9302651 0.6319019 0.025775455 0.0102798908
## 60: 6 ORF60 0.7546193 0.9302651 0.6319019 0.025775455 0.0102798908
## 61: 6 ORF71 0.7546193 0.9302651 0.6319019 0.025775455 0.0102798908
## 62: 6 ORF72 0.7546193 0.9302651 0.6319019 0.025775455 0.0102798908
## 63: 7 ORF19 0.8499612 0.9623404 0.6685152 0.018635343 0.0063920360
## 64: 7 ORF37 0.8499612 0.9623404 0.6685152 0.018635343 0.0063920360
## 65: 7 ORF49 0.8499612 0.9623404 0.6685152 0.018635343 0.0063920360
## 66: 7 ORF51 0.8499612 0.9623404 0.6685152 0.018635343 0.0063920360
## 67: 8 ORF24 0.9948989 0.9992090 0.8706208 0.001303207 0.0002516741
## 68: 8 ORF68 0.9948989 0.9992090 0.8706208 0.001303207 0.0002516741
## 69: 8 ORF74 0.9948989 0.9992090 0.8706208 0.001303207 0.0002516741
## 70: 9 ORF27 0.8452656 0.9779106 0.4508009 0.020208903 0.0041959358
## 71: 9 ORF32 0.8452656 0.9779106 0.4508009 0.020208903 0.0041959358
## 72: 9 ORF59 0.8452656 0.9779106 0.4508009 0.020208903 0.0041959358
## 73: 10 ORF64_1 0.8521517 0.9860876 0.3328321 0.021534613 0.0030460671
## 74: 11 NOIR_1 0.7842390 0.9694991 0.3916821 0.026602976 0.0056301169
## 75: 12 ORF69 0.7429781 0.9317865 0.5931505 0.026686890 0.0100700071
## 76: 12 ORF70 0.7429781 0.9317865 0.5931505 0.026686890 0.0100700071
## cluster gene si au bp se.si se.au
## se.bp v c pchi
## <num> <num> <num> <num>
## 1: 0.002152081 -2.4868295 0.6511067 0.45180383
## 2: 0.002152081 -2.4868295 0.6511067 0.45180383
## 3: 0.002152081 -2.4868295 0.6511067 0.45180383
## 4: 0.002152081 -2.4868295 0.6511067 0.45180383
## 5: 0.002152081 -2.4868295 0.6511067 0.45180383
## 6: 0.002152081 -2.4868295 0.6511067 0.45180383
## 7: 0.002152081 -2.4868295 0.6511067 0.45180383
## 8: 0.002152081 -2.4868295 0.6511067 0.45180383
## 9: 0.002152081 -2.4868295 0.6511067 0.45180383
## 10: 0.002152081 -2.4868295 0.6511067 0.45180383
## 11: 0.004864501 -1.1164337 0.5523848 0.01618970
## 12: 0.004864501 -1.1164337 0.5523848 0.01618970
## 13: 0.004864501 -1.1164337 0.5523848 0.01618970
## 14: 0.004864501 -1.1164337 0.5523848 0.01618970
## 15: 0.004864501 -1.1164337 0.5523848 0.01618970
## 16: 0.004864501 -1.1164337 0.5523848 0.01618970
## 17: 0.004864501 -1.1164337 0.5523848 0.01618970
## 18: 0.004864501 -1.1164337 0.5523848 0.01618970
## 19: 0.004864501 -1.1164337 0.5523848 0.01618970
## 20: 0.004864501 -1.1164337 0.5523848 0.01618970
## 21: 0.004864501 -1.1164337 0.5523848 0.01618970
## 22: 0.004864501 -1.1164337 0.5523848 0.01618970
## 23: 0.004864501 -1.1164337 0.5523848 0.01618970
## 24: 0.004864501 -1.1164337 0.5523848 0.01618970
## 25: 0.003528384 -2.1142499 0.8366451 0.41090035
## 26: 0.003528384 -2.1142499 0.8366451 0.41090035
## 27: 0.003528384 -2.1142499 0.8366451 0.41090035
## 28: 0.003528384 -2.1142499 0.8366451 0.41090035
## 29: 0.003528384 -2.1142499 0.8366451 0.41090035
## 30: 0.003528384 -2.1142499 0.8366451 0.41090035
## 31: 0.003528384 -2.1142499 0.8366451 0.41090035
## 32: 0.003528384 -2.1142499 0.8366451 0.41090035
## 33: 0.005015553 -0.5818054 0.1606180 0.05815236
## 34: 0.005015553 -0.5818054 0.1606180 0.05815236
## 35: 0.005015553 -0.5818054 0.1606180 0.05815236
## 36: 0.005277323 -0.4880865 0.5526595 0.97974651
## 37: 0.005277323 -0.4880865 0.5526595 0.97974651
## 38: 0.005277323 -0.4880865 0.5526595 0.97974651
## 39: 0.005277323 -0.4880865 0.5526595 0.97974651
## 40: 0.005277323 -0.4880865 0.5526595 0.97974651
## 41: 0.005277323 -0.4880865 0.5526595 0.97974651
## 42: 0.005277323 -0.4880865 0.5526595 0.97974651
## 43: 0.005277323 -0.4880865 0.5526595 0.97974651
## 44: 0.005277323 -0.4880865 0.5526595 0.97974651
## 45: 0.005277323 -0.4880865 0.5526595 0.97974651
## 46: 0.005277323 -0.4880865 0.5526595 0.97974651
## 47: 0.005277323 -0.4880865 0.5526595 0.97974651
## 48: 0.005277323 -0.4880865 0.5526595 0.97974651
## 49: 0.005277323 -0.4880865 0.5526595 0.97974651
## 50: 0.005155700 -0.9073314 0.5704366 0.48841392
## 51: 0.005155700 -0.9073314 0.5704366 0.48841392
## 52: 0.005155700 -0.9073314 0.5704366 0.48841392
## 53: 0.005155700 -0.9073314 0.5704366 0.48841392
## 54: 0.005155700 -0.9073314 0.5704366 0.48841392
## 55: 0.005155700 -0.9073314 0.5704366 0.48841392
## 56: 0.005155700 -0.9073314 0.5704366 0.48841392
## 57: 0.005155700 -0.9073314 0.5704366 0.48841392
## 58: 0.005155700 -0.9073314 0.5704366 0.48841392
## 59: 0.005155700 -0.9073314 0.5704366 0.48841392
## 60: 0.005155700 -0.9073314 0.5704366 0.48841392
## 61: 0.005155700 -0.9073314 0.5704366 0.48841392
## 62: 0.005155700 -0.9073314 0.5704366 0.48841392
## 63: 0.005076291 -1.1071663 0.6713495 0.96807380
## 64: 0.005076291 -1.1071663 0.6713495 0.96807380
## 65: 0.005076291 -1.1071663 0.6713495 0.96807380
## 66: 0.005076291 -1.1071663 0.6713495 0.96807380
## 67: 0.003885549 -2.1442641 1.0149336 0.03185429
## 68: 0.003885549 -2.1442641 1.0149336 0.03185429
## 69: 0.003885549 -2.1442641 1.0149336 0.03185429
## 70: 0.005295012 -0.9443758 1.0680139 0.40394260
## 71: 0.005295012 -0.9443758 1.0680139 0.40394260
## 72: 0.005295012 -0.9443758 1.0680139 0.40394260
## 73: 0.004996046 -0.8838204 1.3159266 0.26244569
## 74: 0.005168542 -0.7992724 1.0742100 0.88785752
## 75: 0.005250585 -0.8624429 0.6267861 0.58239230
## 76: 0.005250585 -0.8624429 0.6267861 0.58239230
## se.bp v c pchi
## [1] "ORF48" "ORF19" "ORF49" "ORF69"## [1] 4## [1] "ORF6" "ORF65_1" "ORF67_1" "ORF8" "ORF22" "ORF23" "ORF25"
## [8] "ORF33" "ORF35.5" "ORF36" "CTO" "ORF42" "ORF43" "ORF44"
## [15] "ORF46" "ORF58" "ORF62" "ORF12" "ORF13" "ORF15" "ORF16"
## [22] "ORF35" "ORF41" "ORF48" "ORF52" "ORF54" "ORF57" "ORF60"
## [29] "ORF71" "ORF72" "ORF69" "ORF70"## [1] 32Selected number of clusters: 12
## Key: <cluster>
## cluster gene si au bp se.si se.au
## <int> <char> <num> <num> <num> <num> <num>
## 1: 1 ORF1 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 2: 1 ORF4 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 3: 1 ORF9 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 4: 1 ORF20 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 5: 1 ORF21 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 6: 1 ORF31 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 7: 1 ORF34 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 8: 1 ORF38 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 9: 1 ORF50 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 10: 1 ORF61 0.9966961 0.9991493 0.9668007 0.001237401 0.0003763751
## 11: 2 ORF2 0.8361360 0.9524233 0.7136396 0.019845119 0.0077877677
## 12: 2 ORF3 0.8361360 0.9524233 0.7136396 0.019845119 0.0077877677
## 13: 2 ORF11 0.8361360 0.9524233 0.7136396 0.019845119 0.0077877677
## 14: 2 ORF14 0.8361360 0.9524233 0.7136396 0.019845119 0.0077877677
## 15: 2 ORF18 0.8361360 0.9524233 0.7136396 0.019845119 0.0077877677
## 16: 2 ORF26 0.8361360 0.9524233 0.7136396 0.019845119 0.0077877677
## 17: 2 ORF28 0.8361360 0.9524233 0.7136396 0.019845119 0.0077877677
## 18: 2 ORF29 0.8361360 0.9524233 0.7136396 0.019845119 0.0077877677
## 19: 2 ORF39 0.8361360 0.9524233 0.7136396 0.019845119 0.0077877677
## 20: 2 ORF40 0.8361360 0.9524233 0.7136396 0.019845119 0.0077877677
## 21: 2 ORF66_1 0.8361360 0.9524233 0.7136396 0.019845119 0.0077877677
## 22: 2 ORF73 0.8361360 0.9524233 0.7136396 0.019845119 0.0077877677
## 23: 2 ORF75 0.8361360 0.9524233 0.7136396 0.019845119 0.0077877677
## 24: 2 ORF76 0.8361360 0.9524233 0.7136396 0.019845119 0.0077877677
## 25: 3 ORF5 0.9921335 0.9984157 0.8993056 0.002040977 0.0005060408
## 26: 3 ORF7 0.9921335 0.9984157 0.8993056 0.002040977 0.0005060408
## 27: 3 ORF10 0.9921335 0.9984157 0.8993056 0.002040977 0.0005060408
## 28: 3 ORF17 0.9921335 0.9984157 0.8993056 0.002040977 0.0005060408
## 29: 3 ORF30 0.9921335 0.9984157 0.8993056 0.002040977 0.0005060408
## 30: 3 ORF53 0.9921335 0.9984157 0.8993056 0.002040977 0.0005060408
## 31: 3 ORF63 0.9921335 0.9984157 0.8993056 0.002040977 0.0005060408
## 32: 3 NOIR_2 0.9921335 0.9984157 0.8993056 0.002040977 0.0005060408
## 33: 4 ORF6 0.4752019 0.7710846 0.6631909 0.036465996 0.0232411811
## 34: 4 ORF65_1 0.4752019 0.7710846 0.6631909 0.036465996 0.0232411811
## 35: 4 ORF67_1 0.4752019 0.7710846 0.6631909 0.036465996 0.0232411811
## 36: 5 ORF8 0.4866577 0.8510033 0.4742570 0.039463824 0.0177067445
## 37: 5 ORF22 0.4866577 0.8510033 0.4742570 0.039463824 0.0177067445
## 38: 5 ORF23 0.4866577 0.8510033 0.4742570 0.039463824 0.0177067445
## 39: 5 ORF25 0.4866577 0.8510033 0.4742570 0.039463824 0.0177067445
## 40: 5 ORF33 0.4866577 0.8510033 0.4742570 0.039463824 0.0177067445
## 41: 5 ORF35.5 0.4866577 0.8510033 0.4742570 0.039463824 0.0177067445
## 42: 5 ORF36 0.4866577 0.8510033 0.4742570 0.039463824 0.0177067445
## 43: 5 CTO 0.4866577 0.8510033 0.4742570 0.039463824 0.0177067445
## 44: 5 ORF42 0.4866577 0.8510033 0.4742570 0.039463824 0.0177067445
## 45: 5 ORF43 0.4866577 0.8510033 0.4742570 0.039463824 0.0177067445
## 46: 5 ORF44 0.4866577 0.8510033 0.4742570 0.039463824 0.0177067445
## 47: 5 ORF46 0.4866577 0.8510033 0.4742570 0.039463824 0.0177067445
## 48: 5 ORF58 0.4866577 0.8510033 0.4742570 0.039463824 0.0177067445
## 49: 5 ORF62 0.4866577 0.8510033 0.4742570 0.039463824 0.0177067445
## 50: 6 ORF12 0.7546193 0.9302651 0.6319019 0.025775455 0.0102798908
## 51: 6 ORF13 0.7546193 0.9302651 0.6319019 0.025775455 0.0102798908
## 52: 6 ORF15 0.7546193 0.9302651 0.6319019 0.025775455 0.0102798908
## 53: 6 ORF16 0.7546193 0.9302651 0.6319019 0.025775455 0.0102798908
## 54: 6 ORF35 0.7546193 0.9302651 0.6319019 0.025775455 0.0102798908
## 55: 6 ORF41 0.7546193 0.9302651 0.6319019 0.025775455 0.0102798908
## 56: 6 ORF48 0.7546193 0.9302651 0.6319019 0.025775455 0.0102798908
## 57: 6 ORF52 0.7546193 0.9302651 0.6319019 0.025775455 0.0102798908
## 58: 6 ORF54 0.7546193 0.9302651 0.6319019 0.025775455 0.0102798908
## 59: 6 ORF57 0.7546193 0.9302651 0.6319019 0.025775455 0.0102798908
## 60: 6 ORF60 0.7546193 0.9302651 0.6319019 0.025775455 0.0102798908
## 61: 6 ORF71 0.7546193 0.9302651 0.6319019 0.025775455 0.0102798908
## 62: 6 ORF72 0.7546193 0.9302651 0.6319019 0.025775455 0.0102798908
## 63: 7 ORF19 0.8499612 0.9623404 0.6685152 0.018635343 0.0063920360
## 64: 7 ORF37 0.8499612 0.9623404 0.6685152 0.018635343 0.0063920360
## 65: 7 ORF49 0.8499612 0.9623404 0.6685152 0.018635343 0.0063920360
## 66: 7 ORF51 0.8499612 0.9623404 0.6685152 0.018635343 0.0063920360
## 67: 8 ORF24 0.9948989 0.9992090 0.8706208 0.001303207 0.0002516741
## 68: 8 ORF68 0.9948989 0.9992090 0.8706208 0.001303207 0.0002516741
## 69: 8 ORF74 0.9948989 0.9992090 0.8706208 0.001303207 0.0002516741
## 70: 9 ORF27 0.8452656 0.9779106 0.4508009 0.020208903 0.0041959358
## 71: 9 ORF32 0.8452656 0.9779106 0.4508009 0.020208903 0.0041959358
## 72: 9 ORF59 0.8452656 0.9779106 0.4508009 0.020208903 0.0041959358
## 73: 10 ORF64_1 0.8521517 0.9860876 0.3328321 0.021534613 0.0030460671
## 74: 11 NOIR_1 0.7842390 0.9694991 0.3916821 0.026602976 0.0056301169
## 75: 12 ORF69 0.7429781 0.9317865 0.5931505 0.026686890 0.0100700071
## 76: 12 ORF70 0.7429781 0.9317865 0.5931505 0.026686890 0.0100700071
## cluster gene si au bp se.si se.au
## se.bp v c pchi
## <num> <num> <num> <num>
## 1: 0.002152081 -2.4868295 0.6511067 0.45180383
## 2: 0.002152081 -2.4868295 0.6511067 0.45180383
## 3: 0.002152081 -2.4868295 0.6511067 0.45180383
## 4: 0.002152081 -2.4868295 0.6511067 0.45180383
## 5: 0.002152081 -2.4868295 0.6511067 0.45180383
## 6: 0.002152081 -2.4868295 0.6511067 0.45180383
## 7: 0.002152081 -2.4868295 0.6511067 0.45180383
## 8: 0.002152081 -2.4868295 0.6511067 0.45180383
## 9: 0.002152081 -2.4868295 0.6511067 0.45180383
## 10: 0.002152081 -2.4868295 0.6511067 0.45180383
## 11: 0.004864501 -1.1164337 0.5523848 0.01618970
## 12: 0.004864501 -1.1164337 0.5523848 0.01618970
## 13: 0.004864501 -1.1164337 0.5523848 0.01618970
## 14: 0.004864501 -1.1164337 0.5523848 0.01618970
## 15: 0.004864501 -1.1164337 0.5523848 0.01618970
## 16: 0.004864501 -1.1164337 0.5523848 0.01618970
## 17: 0.004864501 -1.1164337 0.5523848 0.01618970
## 18: 0.004864501 -1.1164337 0.5523848 0.01618970
## 19: 0.004864501 -1.1164337 0.5523848 0.01618970
## 20: 0.004864501 -1.1164337 0.5523848 0.01618970
## 21: 0.004864501 -1.1164337 0.5523848 0.01618970
## 22: 0.004864501 -1.1164337 0.5523848 0.01618970
## 23: 0.004864501 -1.1164337 0.5523848 0.01618970
## 24: 0.004864501 -1.1164337 0.5523848 0.01618970
## 25: 0.003528384 -2.1142499 0.8366451 0.41090035
## 26: 0.003528384 -2.1142499 0.8366451 0.41090035
## 27: 0.003528384 -2.1142499 0.8366451 0.41090035
## 28: 0.003528384 -2.1142499 0.8366451 0.41090035
## 29: 0.003528384 -2.1142499 0.8366451 0.41090035
## 30: 0.003528384 -2.1142499 0.8366451 0.41090035
## 31: 0.003528384 -2.1142499 0.8366451 0.41090035
## 32: 0.003528384 -2.1142499 0.8366451 0.41090035
## 33: 0.005015553 -0.5818054 0.1606180 0.05815236
## 34: 0.005015553 -0.5818054 0.1606180 0.05815236
## 35: 0.005015553 -0.5818054 0.1606180 0.05815236
## 36: 0.005277323 -0.4880865 0.5526595 0.97974651
## 37: 0.005277323 -0.4880865 0.5526595 0.97974651
## 38: 0.005277323 -0.4880865 0.5526595 0.97974651
## 39: 0.005277323 -0.4880865 0.5526595 0.97974651
## 40: 0.005277323 -0.4880865 0.5526595 0.97974651
## 41: 0.005277323 -0.4880865 0.5526595 0.97974651
## 42: 0.005277323 -0.4880865 0.5526595 0.97974651
## 43: 0.005277323 -0.4880865 0.5526595 0.97974651
## 44: 0.005277323 -0.4880865 0.5526595 0.97974651
## 45: 0.005277323 -0.4880865 0.5526595 0.97974651
## 46: 0.005277323 -0.4880865 0.5526595 0.97974651
## 47: 0.005277323 -0.4880865 0.5526595 0.97974651
## 48: 0.005277323 -0.4880865 0.5526595 0.97974651
## 49: 0.005277323 -0.4880865 0.5526595 0.97974651
## 50: 0.005155700 -0.9073314 0.5704366 0.48841392
## 51: 0.005155700 -0.9073314 0.5704366 0.48841392
## 52: 0.005155700 -0.9073314 0.5704366 0.48841392
## 53: 0.005155700 -0.9073314 0.5704366 0.48841392
## 54: 0.005155700 -0.9073314 0.5704366 0.48841392
## 55: 0.005155700 -0.9073314 0.5704366 0.48841392
## 56: 0.005155700 -0.9073314 0.5704366 0.48841392
## 57: 0.005155700 -0.9073314 0.5704366 0.48841392
## 58: 0.005155700 -0.9073314 0.5704366 0.48841392
## 59: 0.005155700 -0.9073314 0.5704366 0.48841392
## 60: 0.005155700 -0.9073314 0.5704366 0.48841392
## 61: 0.005155700 -0.9073314 0.5704366 0.48841392
## 62: 0.005155700 -0.9073314 0.5704366 0.48841392
## 63: 0.005076291 -1.1071663 0.6713495 0.96807380
## 64: 0.005076291 -1.1071663 0.6713495 0.96807380
## 65: 0.005076291 -1.1071663 0.6713495 0.96807380
## 66: 0.005076291 -1.1071663 0.6713495 0.96807380
## 67: 0.003885549 -2.1442641 1.0149336 0.03185429
## 68: 0.003885549 -2.1442641 1.0149336 0.03185429
## 69: 0.003885549 -2.1442641 1.0149336 0.03185429
## 70: 0.005295012 -0.9443758 1.0680139 0.40394260
## 71: 0.005295012 -0.9443758 1.0680139 0.40394260
## 72: 0.005295012 -0.9443758 1.0680139 0.40394260
## 73: 0.004996046 -0.8838204 1.3159266 0.26244569
## 74: 0.005168542 -0.7992724 1.0742100 0.88785752
## 75: 0.005250585 -0.8624429 0.6267861 0.58239230
## 76: 0.005250585 -0.8624429 0.6267861 0.58239230
## se.bp v c pchi
## [1] "ORF48" "ORF19" "ORF49" "ORF69"## [1] 4## [1] "ORF6" "ORF65_1" "ORF67_1" "ORF8" "ORF22" "ORF23" "ORF25"
## [8] "ORF33" "ORF35.5" "ORF36" "CTO" "ORF42" "ORF43" "ORF44"
## [15] "ORF46" "ORF58" "ORF62" "ORF12" "ORF13" "ORF15" "ORF16"
## [22] "ORF35" "ORF41" "ORF48" "ORF52" "ORF54" "ORF57" "ORF60"
## [29] "ORF71" "ORF72" "ORF69" "ORF70"## [1] 32Remove genes from clusters ?
## [1] "ORF6" "ORF65_1" "ORF67_1" "ORF8" "ORF22" "ORF23" "ORF25"
## [8] "ORF33" "ORF35.5" "ORF36" "CTO" "ORF42" "ORF43" "ORF44"
## [15] "ORF46" "ORF58" "ORF62" "ORF12" "ORF13" "ORF15" "ORF16"
## [22] "ORF35" "ORF41" "ORF48" "ORF52" "ORF54" "ORF57" "ORF60"
## [29] "ORF71" "ORF72" "ORF69" "ORF70"## [1] 32## No genes were removed from their corresponding clusters.## cluster N
## <int> <int>
## 1: 2 14
## 2: 5 14
## 3: 6 13
## 4: 1 10
## 5: 3 8
## 6: 7 4
## 7: 4 3
## 8: 8 3
## 9: 9 3
## 10: 12 2
## 11: 10 1
## 12: 11 1Merge cluster stats
Assigning genes to clusters
Summarize and melt
Heatmaps
Normalized Expression
Expression delta ~ 6 hpi
Z-score of expression delta ~ 6 hpi
ORF kinetics, according to literature-based kinetic classes
Barplot of mean and SD
Figure 4 REVIEW - Mean and SD with linear connection
Mean and SD with loess function
Mean and SD with linear connection - Figure 4
Each replicate with loess
ORF kinetics, according to de-novo kinetic classes
Mean and SD with linear connection
Figure 5 REVIEW - Mean and SD with linear connection
Compare literature and de novo kinetic classes
NA shows the number of genes where the clustering did not yield an unambiguous result.
Combined Kinetic classes
De Novo Clusters
Literature clusters
